src/jalview/gui/Preferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import java.awt.BorderLayout;
  24 import java.awt.Color;
  25 import java.awt.Component;
  26 import java.awt.Dimension;
  27 import java.awt.Font;
  28 import java.awt.event.ActionEvent;
  29 import java.awt.event.ActionListener;
  30 import java.awt.event.MouseEvent;
  31 import java.io.File;
  32 import java.util.ArrayList;
  33 import java.util.List;
  34 import java.util.concurrent.CompletableFuture;
  35
  36 import javax.help.HelpSetException;
  37 import javax.swing.JComboBox;
  38 import javax.swing.JFileChooser;
  39 import javax.swing.JInternalFrame;
  40 import javax.swing.JPanel;
  41 import javax.swing.ListSelectionModel;
  42 import javax.swing.RowFilter;
  43 import javax.swing.RowSorter;
  44 import javax.swing.SortOrder;
  45 import javax.swing.event.DocumentEvent;
  46 import javax.swing.event.DocumentListener;
  47 import javax.swing.event.ListSelectionEvent;
  48 import javax.swing.event.ListSelectionListener;
  49 import javax.swing.table.TableCellRenderer;
  50 import javax.swing.table.TableColumn;
  51 import javax.swing.table.TableModel;
  52 import javax.swing.table.TableRowSorter;
  53
  54 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  55 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  56 import jalview.bin.Cache;
  57 import jalview.bin.MemorySetting;
  58 import jalview.ext.pymol.PymolManager;
  59 import jalview.gui.Help.HelpId;
  60 import jalview.gui.StructureViewer.ViewerType;
  61 import jalview.io.BackupFiles;
  62 import jalview.io.BackupFilesPresetEntry;
  63 import jalview.io.FileFormatI;
  64 import jalview.io.JalviewFileChooser;
  65 import jalview.io.JalviewFileView;
  66 import jalview.jbgui.GPreferences;
  67 import jalview.jbgui.GSequenceLink;
  68 import jalview.schemes.ColourSchemeI;
  69 import jalview.schemes.ColourSchemes;
  70 import jalview.schemes.ResidueColourScheme;
  71 import jalview.urls.UrlLinkTableModel;
  72 import jalview.urls.api.UrlProviderFactoryI;
  73 import jalview.urls.api.UrlProviderI;
  74 import jalview.urls.desktop.DesktopUrlProviderFactory;
  75 import jalview.util.MessageManager;
  76 import jalview.util.Platform;
  77 import jalview.util.UrlConstants;
  78 import jalview.ws.sifts.SiftsSettings;
  79
  80 /**
  81  * DOCUMENT ME!
  82  *
  83  * @author $author$
  84  * @version $Revision$
  85  */
  86 /*
  87  * for merge with Jalview-JS
  88  public class Preferences extends GPreferences implements ApplicationSingletonI
  89  */
  90 public class Preferences extends GPreferences
  91 {
  92   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  93
  94   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  95
  96   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  97
  98   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  99
 100   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
 101
 102   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
 103
 104   public static final String ADD_SS_ANN = "ADD_SS_ANN";
 105
 106   public static final String USE_RNAVIEW = "USE_RNAVIEW";
 107
 108   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 109
 110   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 111
 112   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 113
 114   public static final String CHIMERAX_PATH = "CHIMERAX_PATH";
 115
 116   public static final String PYMOL_PATH = "PYMOL_PATH";
 117
 118   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 119
 120   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 121
 122   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 123
 124   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 125
 126   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 127
 128   public static final String GAP_COLOUR = "GAP_COLOUR";
 129
 130   public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 131
 132   private static final int MIN_FONT_SIZE = 1;
 133
 134   private static final int MAX_FONT_SIZE = 30;
 135
 136   private String previousProxyType;
 137
 138   private static Preferences INSTANCE = null; // add "final"
 139
 140   /**
 141    * Holds name and link separated with | character. Sequence ID must be
 142    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 143    */
 144   public static UrlProviderI sequenceUrlLinks;
 145
 146   public static UrlLinkTableModel dataModel;
 147
 148   /**
 149    * Holds name and link separated with | character. Sequence IDS and Sequences
 150    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and $SEQUENCES$
 151    * or $SEQUENCES=/.possible | chars ./=$ and separation character for first and
 152    * second token specified after a pipe character at end |,|. (TODO: proper
 153    * escape for using | to separate ids or sequences
 154    */
 155
 156   public static List<String> groupURLLinks;
 157   static
 158   {
 159     // get links selected to be in the menu (SEQUENCE_LINKS)
 160     // and links entered by the user but not selected (STORED_LINKS)
 161     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 162     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 163     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 164             UrlConstants.DEFAULT_LABEL);
 165
 166     // if both links lists are empty, add the DEFAULT_URL link
 167     // otherwise we assume the default link is in one of the lists
 168     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 169     {
 170       inMenuString = UrlConstants.DEFAULT_STRING;
 171     }
 172     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 173             inMenuString, notInMenuString);
 174     sequenceUrlLinks = factory.createUrlProvider();
 175     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 176
 177     /**
 178      * TODO: reformulate groupURL encoding so two or more can be stored in the
 179      * .properties file as '|' separated strings
 180      */
 181
 182     groupURLLinks = new ArrayList<>();
 183   }
 184
 185   JInternalFrame frame;
 186
 187   private WsPreferences wsPrefs;
 188
 189   private OptionsParam promptEachTimeOpt = new OptionsParam(
 190           MessageManager.getString("label.prompt_each_time"),
 191           "Prompt each time");
 192
 193   private OptionsParam lineArtOpt = new OptionsParam(
 194           MessageManager.getString("label.lineart"), "Lineart");
 195
 196   private OptionsParam textOpt = new OptionsParam(
 197           MessageManager.getString("action.text"), "Text");
 198
 199   // get singleton Preferences instance
 200   public static Preferences getInstance()
 201   {
 202     if (INSTANCE == null || INSTANCE.frame == null
 203             || INSTANCE.frame.isClosed())
 204     {
 205       INSTANCE = new Preferences();
 206     }
 207     return INSTANCE;
 208
 209     /*
 210      * Replace code with the following for Jalvew-JS
 211     Preferences INSTANCE = ApplicationSingletonProvider.getInstance(Preferences.class);
 212     if (INSTANCE == null || INSTANCE.frame == null
 213             || INSTANCE.frame.isClosed())
 214     {
 215       ApplicationSingletonProvider.remove(Preferences.class);
 216       INSTANCE = ApplicationSingletonProvider.getInstance(Preferences.class);
 217     }
 218     return INSTANCE;
 219     */
 220   }
 221
 222   public static void openPreferences()
 223   {
 224     openPreferences(null, null);
 225   }
 226
 227   public static void openPreferences(TabRef selectTab, String message)
 228   {
 229     Preferences p = getInstance();
 230     if (selectTab != null)
 231       p.selectTab(selectTab, message);
 232     p.frame.show();
 233     p.frame.moveToFront();
 234     p.frame.grabFocus();
 235   }
 236
 237   public void selectTab(TabRef selectTab, String message)
 238   {
 239     this.selectTab(selectTab);
 240     if (message != null)
 241       this.setMessage(message);
 242     this.frame.show();
 243   }
 244
 245   /**
 246    * Creates a new Preferences object.
 247    */
 248   private Preferences()
 249   {
 250     super();
 251     frame = new JInternalFrame();
 252     frame.setContentPane(this);
 253     if (!Platform.isJS())
 254     /**
 255      * Java only
 256      *
 257      * @j2sIgnore
 258      */
 259     {
 260       wsPrefs = new WsPreferences();
 261       wsTab.add(wsPrefs, BorderLayout.CENTER);
 262     }
 263     int width = 500, height = 450;
 264     if (Platform.isAMacAndNotJS())
 265     {
 266       width = 570;
 267       height = 480;
 268     }
 269
 270     Desktop.addInternalFrame(frame,
 271             MessageManager.getString("label.preferences"), width, height);
 272     frame.setMinimumSize(new Dimension(width, height));
 273
 274     /*
 275      * Set Visual tab defaults
 276      */
 277     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 278     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 279     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 280     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 281
 282     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 283     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 284     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 285     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 286     showUnconserved
 287             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 288     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 289     showGroupConsensus
 290             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 291     showGroupConservation.setSelected(
 292             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 293     showConsensHistogram.setSelected(
 294             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 295     showConsensLogo
 296             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 297     showNpTooltip
 298             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 299     showDbRefTooltip
 300             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 301
 302     String[] fonts = java.awt.GraphicsEnvironment
 303             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 304     for (int i = 0; i < fonts.length; i++)
 305     {
 306       fontNameCB.addItem(fonts[i]);
 307     }
 308
 309     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 310     {
 311       fontSizeCB.addItem(i + "");
 312     }
 313
 314     fontStyleCB.addItem("plain");
 315     fontStyleCB.addItem("bold");
 316     fontStyleCB.addItem("italic");
 317
 318     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 319     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 320     fontStyleCB.setSelectedItem(
 321             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 322
 323     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
 324     scaleProteinToCdna
 325             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 326
 327     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 328
 329     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 330
 331     gapSymbolCB.addItem("-");
 332     gapSymbolCB.addItem(".");
 333
 334     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 335
 336     sortby.addItem("No sort");
 337     sortby.addItem("Id");
 338     sortby.addItem("Pairwise Identity");
 339     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 340
 341     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 342     sortAnnBy
 343             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 344     sortAnnBy
 345             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 346     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 347             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 348                     SequenceAnnotationOrder.NONE.name()));
 349     sortAnnBy.setSelectedItem(savedSort.toString());
 350
 351     sortAutocalc.addItem("Autocalculated first");
 352     sortAutocalc.addItem("Autocalculated last");
 353     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 354     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 355             : sortAutocalc.getItemAt(1));
 356     startupCheckbox
 357             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 358     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 359             Cache.getDefault("www.jalview.org", "https://www.jalview.org")
 360                     + "/examples/exampleFile_2_7.jvp"));
 361
 362     /*
 363      * Set Colours tab defaults
 364      */
 365     protColour.addItem(ResidueColourScheme.NONE);
 366     nucColour.addItem(ResidueColourScheme.NONE);
 367     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 368     {
 369       String name = cs.getSchemeName();
 370       protColour.addItem(name);
 371       nucColour.addItem(name);
 372     }
 373     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 374             ResidueColourScheme.NONE);
 375     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 376     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 377     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 378     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 379     minColour.setBackground(
 380             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 381     maxColour.setBackground(
 382             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 383
 384     /*
 385      * Set overview panel defaults
 386      */
 387     gapColour.setBackground(Cache.getDefaultColour(GAP_COLOUR,
 388             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 389     hiddenColour.setBackground(Cache.getDefaultColour(HIDDEN_COLOUR,
 390             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 391     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 392     gapLabel.setEnabled(!useLegacyGap.isSelected());
 393     gapColour.setEnabled(!useLegacyGap.isSelected());
 394     showHiddenAtStart
 395             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 396
 397     /*
 398      * Set Structure tab defaults
 399      */
 400     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, true);
 401     structFromPdb.setSelected(structSelected);
 402     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, true));
 403     addSecondaryStructure.setEnabled(structSelected);
 404     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, true));
 405     addTempFactor.setEnabled(structSelected);
 406
 407     /*
 408      * set choice of structure viewer, and path if saved as a preference;
 409      * default to Jmol (first choice) if an unexpected value is found
 410      */
 411     String viewerType = Cache.getDefault(STRUCTURE_DISPLAY,
 412             ViewerType.JMOL.name());
 413     structViewer.setSelectedItem(viewerType);
 414     String viewerPath = "";
 415     ViewerType type = null;
 416     try
 417     {
 418       type = ViewerType.valueOf(viewerType);
 419       switch (type)
 420       {
 421       case JMOL:
 422         break;
 423       case CHIMERA:
 424         viewerPath = Cache.getDefault(CHIMERA_PATH, "");
 425         break;
 426       case CHIMERAX:
 427         viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
 428         break;
 429       case PYMOL:
 430         viewerPath = Cache.getDefault(PYMOL_PATH, "");
 431         break;
 432       }
 433     } catch (IllegalArgumentException e)
 434     {
 435       Cache.error("Unknown structure viewer type: " + viewerType
 436               + ", defaulting to Jmol");
 437       type = ViewerType.JMOL;
 438     }
 439     structureViewerPath.setText(viewerPath);
 440
 441     structureViewerPath.addActionListener(new ActionListener()
 442     {
 443       @Override
 444       public void actionPerformed(ActionEvent e)
 445       {
 446         if (validateViewerPath())
 447         {
 448           String path = structureViewerPath.getText();
 449           try {
 450           ViewerType type = ViewerType.valueOf(viewerType);
 451           switch (type)
 452           {
 453           case JMOL:
 454             break;
 455           case CHIMERA:
 456             Cache.setProperty(CHIMERA_PATH, path);
 457             break;
 458           case CHIMERAX:
 459             Cache.setProperty(CHIMERAX_PATH, path);
 460             break;
 461           case PYMOL:
 462             Cache.setProperty(PYMOL_PATH, path);
 463             break;
 464           }
 465         } catch (IllegalArgumentException x)
 466         {
 467           Cache.error("Failed to set path - unknown viewer type",x);
 468         }
 469         }
 470       }
 471     });
 472
 473     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 474     {
 475       siftsMapping.setSelected(true);
 476     }
 477     else
 478     {
 479       nwMapping.setSelected(true);
 480     }
 481
 482     SiftsSettings
 483             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 484
 485     /*
 486      * Set Connections tab defaults
 487      */
 488
 489     // set up sorting
 490     linkUrlTable.setModel(dataModel);
 491     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 492             linkUrlTable.getModel());
 493     linkUrlTable.setRowSorter(sorter);
 494     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 495
 496     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 497     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 498             SortOrder.DESCENDING));
 499     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 500             SortOrder.DESCENDING));
 501     sortKeys.add(
 502             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 503
 504     sorter.setSortKeys(sortKeys);
 505     // BH 2018 setSortKeys will do the sort
 506     // sorter.sort();
 507
 508     // set up filtering
 509     ActionListener onReset;
 510     onReset = new ActionListener()
 511     {
 512       @Override
 513       public void actionPerformed(ActionEvent e)
 514       {
 515         filterTB.setText("");
 516         sorter.setRowFilter(RowFilter.regexFilter(""));
 517       }
 518
 519     };
 520     doReset.addActionListener(onReset);
 521
 522     // filter to display only custom urls
 523     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 524     {
 525       @Override
 526       public boolean include(
 527               Entry<? extends TableModel, ? extends Object> entry)
 528       {
 529         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 530       }
 531     };
 532
 533     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 534             linkUrlTable.getModel());
 535     customSorter.setRowFilter(customUrlFilter);
 536
 537     ActionListener onCustomOnly;
 538     onCustomOnly = new ActionListener()
 539     {
 540       @Override
 541       public void actionPerformed(ActionEvent e)
 542       {
 543         filterTB.setText("");
 544         sorter.setRowFilter(customUrlFilter);
 545       }
 546     };
 547     userOnly.addActionListener(onCustomOnly);
 548
 549     filterTB.getDocument().addDocumentListener(new DocumentListener()
 550     {
 551       String caseInsensitiveFlag = "(?i)";
 552
 553       @Override
 554       public void changedUpdate(DocumentEvent e)
 555       {
 556         sorter.setRowFilter(RowFilter
 557                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 558       }
 559
 560       @Override
 561       public void removeUpdate(DocumentEvent e)
 562       {
 563         sorter.setRowFilter(RowFilter
 564                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 565       }
 566
 567       @Override
 568       public void insertUpdate(DocumentEvent e)
 569       {
 570         sorter.setRowFilter(RowFilter
 571                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 572       }
 573     });
 574
 575     // set up list selection functionality
 576     linkUrlTable.getSelectionModel()
 577             .addListSelectionListener(new UrlListSelectionHandler());
 578
 579     // set up radio buttons
 580     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 581             .getPrimaryColumn();
 582     String onClickName = linkUrlTable.getColumnName(onClickCol);
 583     linkUrlTable.getColumn(onClickName)
 584             .setCellRenderer(new RadioButtonRenderer());
 585     linkUrlTable.getColumn(onClickName)
 586             .setCellEditor(new RadioButtonEditor());
 587
 588     // get boolean columns and resize those to min possible
 589     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 590     {
 591       if (linkUrlTable.getModel().getColumnClass(column)
 592               .equals(Boolean.class))
 593       {
 594         TableColumn tableColumn = linkUrlTable.getColumnModel()
 595                 .getColumn(column);
 596         int preferredWidth = tableColumn.getMinWidth();
 597
 598         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 599                 column);
 600         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 601         int cwidth = c.getPreferredSize().width
 602                 + linkUrlTable.getIntercellSpacing().width;
 603         preferredWidth = Math.max(preferredWidth, cwidth);
 604
 605         tableColumn.setPreferredWidth(preferredWidth);
 606       }
 607     }
 608
 609     String proxyTypeString = Cache.getDefault("USE_PROXY", "false");
 610     previousProxyType = proxyTypeString;
 611     switch (proxyTypeString)
 612     {
 613     case Cache.PROXYTYPE_NONE:
 614       proxyType.setSelected(noProxy.getModel(), true);
 615       break;
 616     case Cache.PROXYTYPE_SYSTEM:
 617       proxyType.setSelected(systemProxy.getModel(), true);
 618       break;
 619     case Cache.PROXYTYPE_CUSTOM:
 620       proxyType.setSelected(customProxy.getModel(), true);
 621       break;
 622     default:
 623       Cache.warn(
 624               "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
 625                       + proxyTypeString);
 626     }
 627     proxyServerHttpTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 628     proxyPortHttpTB.setText(Cache.getDefault("PROXY_PORT", ""));
 629     proxyServerHttpsTB.setText(Cache.getDefault("PROXY_SERVER_HTTPS", ""));
 630     proxyPortHttpsTB.setText(Cache.getDefault("PROXY_PORT_HTTPS", ""));
 631     proxyAuth.setSelected(Cache.getDefault("PROXY_AUTH", false));
 632     proxyAuthUsernameTB
 633             .setText(Cache.getDefault("PROXY_AUTH_USERNAME", ""));
 634     // we are not storing or retrieving proxy password from .jalview_properties
 635     proxyAuthPasswordPB.setText(Cache.proxyAuthPassword == null ? ""
 636             : new String(Cache.proxyAuthPassword));
 637     setCustomProxyEnabled();
 638     applyProxyButtonEnabled(false);
 639
 640     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 641
 642     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 643     // note antisense here: default is true
 644     questionnaire
 645             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 646     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 647
 648     /*
 649      * Set Output tab defaults
 650      */
 651     setupOutputCombo(epsRendering, "EPS_RENDERING");
 652     setupOutputCombo(htmlRendering, "HTML_RENDERING");
 653     setupOutputCombo(svgRendering, "SVG_RENDERING");
 654     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 655     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 656     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 657     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 658     userIdWidth.setText(wi == null ? "" : wi.toString());
 659     // TODO: refactor to use common enum via FormatAdapter and allow extension
 660     // for new flat file formats
 661     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 662     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 663     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 664     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 665     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 666     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 667     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 668     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 669     embbedBioJSON
 670             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 671
 672     /*
 673      * Set Editing tab defaults
 674      */
 675     autoCalculateConsCheck
 676             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 677     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 678     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 679
 680     annotations_actionPerformed(null); // update the display of the annotation
 681                                        // settings
 682
 683     /*
 684      * Set Backups tab defaults
 685      */
 686     loadLastSavedBackupsOptions();
 687
 688     /*
 689      * Set Startup tab defaults
 690      */
 691
 692   }
 693
 694   /**
 695    * A helper method that sets the items and initial selection in a character
 696    * rendering option list (Prompt each time/Lineart/Text)
 697    *
 698    * @param comboBox
 699    * @param propertyKey
 700    */
 701   protected void setupOutputCombo(JComboBox<Object> comboBox,
 702           String propertyKey)
 703   {
 704     comboBox.addItem(promptEachTimeOpt);
 705     comboBox.addItem(lineArtOpt);
 706     comboBox.addItem(textOpt);
 707
 708     /*
 709      * JalviewJS doesn't support Lineart so force it to Text
 710      */
 711     String defaultOption = Platform.isJS() ? "Text"
 712             : Cache.getDefault(propertyKey, "Prompt each time");
 713     if (defaultOption.equalsIgnoreCase("Text"))
 714     {
 715       comboBox.setSelectedItem(textOpt);
 716     }
 717     else if (defaultOption.equalsIgnoreCase("Lineart"))
 718     {
 719       comboBox.setSelectedItem(lineArtOpt);
 720     }
 721     else
 722     {
 723       comboBox.setSelectedItem(promptEachTimeOpt);
 724     }
 725   }
 726
 727   /**
 728    * Save user selections on the Preferences tabs to the Cache and write out to
 729    * file.
 730    *
 731    * @param e
 732    */
 733   @Override
 734   public void ok_actionPerformed(ActionEvent e)
 735   {
 736     if (!validateSettings())
 737     {
 738       return;
 739     }
 740
 741     /*
 742      * Set proxy settings first (to be before web services refresh)
 743      */
 744     saveProxySettings();
 745
 746     /*
 747      * Save Visual settings
 748      */
 749     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 750             Boolean.toString(seqLimit.isSelected()));
 751     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 752             Boolean.toString(rightAlign.isSelected()));
 753     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 754             Boolean.toString(fullScreen.isSelected()));
 755     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 756             Boolean.toString(openoverv.isSelected()));
 757     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 758             Boolean.toString(annotations.isSelected()));
 759     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 760             Boolean.toString(conservation.isSelected()));
 761     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 762             Boolean.toString(quality.isSelected()));
 763     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 764             Boolean.toString(identity.isSelected()));
 765
 766     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 767             gapSymbolCB.getSelectedItem().toString());
 768
 769     Cache.applicationProperties.setProperty("FONT_NAME",
 770             fontNameCB.getSelectedItem().toString());
 771     Cache.applicationProperties.setProperty("FONT_STYLE",
 772             fontStyleCB.getSelectedItem().toString());
 773     Cache.applicationProperties.setProperty("FONT_SIZE",
 774             fontSizeCB.getSelectedItem().toString());
 775
 776     Cache.applicationProperties.setProperty("ID_ITALICS",
 777             Boolean.toString(idItalics.isSelected()));
 778     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 779             Boolean.toString(showUnconserved.isSelected()));
 780     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 781             Boolean.toString(showOccupancy.isSelected()));
 782     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 783             Boolean.toString(showGroupConsensus.isSelected()));
 784     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 785             Boolean.toString(showGroupConservation.isSelected()));
 786     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 787             Boolean.toString(showConsensHistogram.isSelected()));
 788     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 789             Boolean.toString(showConsensLogo.isSelected()));
 790     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 791             Boolean.toString(smoothFont.isSelected()));
 792     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 793             Boolean.toString(scaleProteinToCdna.isSelected()));
 794     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 795             Boolean.toString(showNpTooltip.isSelected()));
 796     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 797             Boolean.toString(showDbRefTooltip.isSelected()));
 798
 799     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 800             Boolean.toString(wrap.isSelected()));
 801
 802     Cache.applicationProperties.setProperty("STARTUP_FILE",
 803             startupFileTextfield.getText());
 804     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 805             Boolean.toString(startupCheckbox.isSelected()));
 806
 807     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 808             sortby.getSelectedItem().toString());
 809
 810     // convert description of sort order to enum name for save
 811     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 812             .forDescription(sortAnnBy.getSelectedItem().toString());
 813     if (annSortOrder != null)
 814     {
 815       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 816               annSortOrder.name());
 817     }
 818
 819     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 820     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 821             Boolean.valueOf(showAutocalcFirst).toString());
 822
 823     /*
 824      * Save Colours settings
 825      */
 826     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 827             protColour.getSelectedItem().toString());
 828     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 829             nucColour.getSelectedItem().toString());
 830     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 831             minColour.getBackground());
 832     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 833             maxColour.getBackground());
 834
 835     /*
 836      * Save Overview settings
 837      */
 838     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 839     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 840     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 841             Boolean.toString(useLegacyGap.isSelected()));
 842     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 843             Boolean.toString(showHiddenAtStart.isSelected()));
 844
 845     /*
 846      * Save Structure settings
 847      */
 848     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 849             Boolean.toString(addTempFactor.isSelected()));
 850     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 851             Boolean.toString(addSecondaryStructure.isSelected()));
 852     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 853             Boolean.toString(structFromPdb.isSelected()));
 854     String viewer = structViewer.getSelectedItem().toString();
 855     String viewerPath = structureViewerPath.getText();
 856     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, viewer);
 857     if (viewer.equals(ViewerType.CHIMERA.name()))
 858     {
 859       Cache.setOrRemove(CHIMERA_PATH, viewerPath);
 860     }
 861     else if (viewer.equals(ViewerType.CHIMERAX.name()))
 862     {
 863       Cache.setOrRemove(CHIMERAX_PATH, viewerPath);
 864     }
 865     else if (viewer.equals(ViewerType.PYMOL.name()))
 866     {
 867       Cache.setOrRemove(PYMOL_PATH, viewerPath);
 868     }
 869     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 870             Boolean.toString(siftsMapping.isSelected()));
 871     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 872
 873     /*
 874      * Save Output settings
 875      */
 876     Cache.applicationProperties.setProperty("EPS_RENDERING",
 877             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 878     Cache.applicationProperties.setProperty("HTML_RENDERING",
 879             ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
 880     Cache.applicationProperties.setProperty("SVG_RENDERING",
 881             ((OptionsParam) svgRendering.getSelectedItem()).getCode());
 882
 883     /*
 884      * Save Connections settings
 885      */
 886     // Proxy settings set first (to catch web services)
 887
 888     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 889
 890     jalview.util.BrowserLauncher.resetBrowser();
 891
 892     // save user-defined and selected links
 893     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 894     if (menuLinks.isEmpty())
 895     {
 896       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 897     }
 898     else
 899     {
 900       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 901               menuLinks.toString());
 902     }
 903
 904     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 905     if (nonMenuLinks.isEmpty())
 906     {
 907       Cache.applicationProperties.remove("STORED_LINKS");
 908     }
 909     else
 910     {
 911       Cache.applicationProperties.setProperty("STORED_LINKS",
 912               nonMenuLinks.toString());
 913     }
 914
 915     Cache.applicationProperties.setProperty("DEFAULT_URL",
 916             sequenceUrlLinks.getPrimaryUrlId());
 917
 918     Cache.setProperty("VERSION_CHECK",
 919             Boolean.toString(versioncheck.isSelected()));
 920     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 921     {
 922       // default is false - we only set this if the user has actively agreed
 923       Cache.setProperty("USAGESTATS",
 924               Boolean.toString(usagestats.isSelected()));
 925     }
 926     if (!questionnaire.isSelected())
 927     {
 928       Cache.setProperty("NOQUESTIONNAIRES", "true");
 929     }
 930     else
 931     {
 932       // special - made easy to edit a property file to disable questionnaires
 933       // by just adding the given line
 934       Cache.removeProperty("NOQUESTIONNAIRES");
 935     }
 936
 937     /*
 938      * Save Output settings
 939      */
 940     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 941             Boolean.toString(blcjv.isSelected()));
 942     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 943             Boolean.toString(clustaljv.isSelected()));
 944     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 945             Boolean.toString(fastajv.isSelected()));
 946     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 947             Boolean.toString(msfjv.isSelected()));
 948     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 949             Boolean.toString(pfamjv.isSelected()));
 950     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 951             Boolean.toString(pileupjv.isSelected()));
 952     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 953             Boolean.toString(pirjv.isSelected()));
 954     Cache.applicationProperties.setProperty("PIR_MODELLER",
 955             Boolean.toString(modellerOutput.isSelected()));
 956     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 957             Boolean.toString(embbedBioJSON.isSelected()));
 958     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 959
 960     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 961             Boolean.toString(autoIdWidth.isSelected()));
 962     userIdWidth_actionPerformed();
 963     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 964             userIdWidth.getText());
 965
 966     /*
 967      * Save Editing settings
 968      */
 969     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 970             Boolean.toString(autoCalculateConsCheck.isSelected()));
 971     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 972             Boolean.toString(sortByTree.isSelected()));
 973     Cache.applicationProperties.setProperty("PAD_GAPS",
 974             Boolean.toString(padGaps.isSelected()));
 975
 976     if (!Platform.isJS())
 977     {
 978       wsPrefs.updateAndRefreshWsMenuConfig(false);
 979     }
 980
 981     /*
 982      * Save Backups settings
 983      */
 984     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 985             Boolean.toString(enableBackupFiles.isSelected()));
 986     int preset = getComboIntStringKey(backupfilesPresetsCombo);
 987     Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET",
 988             Integer.toString(preset));
 989
 990     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
 991     {
 992       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
 993       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
 994               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
 995       Cache.applicationProperties.setProperty(
 996               BackupFilesPresetEntry.CUSTOMCONFIG, customBFPE.toString());
 997     }
 998
 999     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
1000             .get(preset);
1001     Cache.applicationProperties.setProperty(
1002             BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
1003
1004     /*
1005      * Save Memory Settings
1006      */
1007     Cache.applicationProperties.setProperty(
1008             MemorySetting.CUSTOMISED_SETTINGS,
1009             Boolean.toString(customiseMemorySetting.isSelected()));
1010     Cache.applicationProperties.setProperty(MemorySetting.MEMORY_JVMMEMPC,
1011             Integer.toString(jvmMemoryPercentSlider.getValue()));
1012     Cache.applicationProperties.setProperty(MemorySetting.MEMORY_JVMMEMMAX,
1013             jvmMemoryMaxTextField.getText());
1014
1015     /*
1016      * save and close Preferences
1017      */
1018
1019     Cache.saveProperties();
1020     Desktop.instance.doConfigureStructurePrefs();
1021     try
1022     {
1023       frame.setClosed(true);
1024     } catch (Exception ex)
1025     {
1026     }
1027   }
1028
1029   public void saveProxySettings()
1030   {
1031     String newProxyType = customProxy.isSelected() ? Cache.PROXYTYPE_CUSTOM
1032             : noProxy.isSelected() ? Cache.PROXYTYPE_NONE
1033                     : Cache.PROXYTYPE_SYSTEM;
1034     Cache.applicationProperties.setProperty("USE_PROXY", newProxyType);
1035     Cache.setOrRemove("PROXY_SERVER", proxyServerHttpTB.getText());
1036     Cache.setOrRemove("PROXY_PORT", proxyPortHttpTB.getText());
1037     Cache.setOrRemove("PROXY_SERVER_HTTPS", proxyServerHttpsTB.getText());
1038     Cache.setOrRemove("PROXY_PORT_HTTPS", proxyPortHttpsTB.getText());
1039     Cache.setOrRemove("PROXY_AUTH",
1040             Boolean.toString(proxyAuth.isSelected()));
1041     Cache.setOrRemove("PROXY_AUTH_USERNAME", proxyAuthUsernameTB.getText());
1042     Cache.proxyAuthPassword = proxyAuthPasswordPB.getPassword();
1043     Cache.setProxyPropertiesFromPreferences(previousProxyType);
1044     if (newProxyType.equals(Cache.PROXYTYPE_CUSTOM)
1045             || !newProxyType.equals(previousProxyType))
1046     {
1047       // force a re-lookup of ws if proxytype is custom or has changed
1048       wsPrefs.update++;
1049     }
1050     previousProxyType = newProxyType;
1051   }
1052
1053   /**
1054    * Do any necessary validation before saving settings. Return focus to the first
1055    * tab which fails validation.
1056    *
1057    * @return
1058    */
1059   private boolean validateSettings()
1060   {
1061     if (!validateStructure())
1062     {
1063       structureTab.requestFocusInWindow();
1064       return false;
1065     }
1066     return true;
1067   }
1068
1069   @Override
1070   protected boolean validateStructure()
1071   {
1072     return validateViewerPath();
1073
1074   }
1075
1076   /**
1077    * DOCUMENT ME!
1078    */
1079   @Override
1080   public void startupFileTextfield_mouseClicked()
1081   {
1082     // TODO: JAL-3048 not needed for Jalview-JS
1083     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
1084     JalviewFileChooser chooser = JalviewFileChooser
1085             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
1086     chooser.setFileView(new JalviewFileView());
1087     chooser.setDialogTitle(
1088             MessageManager.getString("label.select_startup_file"));
1089
1090     int value = chooser.showOpenDialog(this);
1091
1092     if (value == JalviewFileChooser.APPROVE_OPTION)
1093     {
1094       FileFormatI format = chooser.getSelectedFormat();
1095       if (format != null)
1096       {
1097         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
1098                 format.getName());
1099       }
1100       startupFileTextfield
1101               .setText(chooser.getSelectedFile().getAbsolutePath());
1102     }
1103   }
1104
1105   /**
1106    * DOCUMENT ME!
1107    *
1108    * @param e
1109    *            DOCUMENT ME!
1110    */
1111   @Override
1112   public void cancel_actionPerformed(ActionEvent e)
1113   {
1114     try
1115     {
1116       if (!Platform.isJS())
1117       {
1118         wsPrefs.updateWsMenuConfig(true);
1119         wsPrefs.refreshWs_actionPerformed(e);
1120       }
1121       frame.setClosed(true);
1122     } catch (Exception ex)
1123     {
1124     }
1125   }
1126
1127   /**
1128    * DOCUMENT ME!
1129    *
1130    * @param e
1131    *            DOCUMENT ME!
1132    */
1133   @Override
1134   public void annotations_actionPerformed(ActionEvent e)
1135   {
1136     conservation.setEnabled(annotations.isSelected());
1137     quality.setEnabled(annotations.isSelected());
1138     identity.setEnabled(annotations.isSelected());
1139     showOccupancy.setEnabled(annotations.isSelected());
1140     showGroupConsensus.setEnabled(annotations.isSelected());
1141     showGroupConservation.setEnabled(annotations.isSelected());
1142     showConsensHistogram.setEnabled(annotations.isSelected()
1143             && (identity.isSelected() || showGroupConsensus.isSelected()));
1144     showConsensLogo.setEnabled(annotations.isSelected()
1145             && (identity.isSelected() || showGroupConsensus.isSelected()));
1146   }
1147
1148   @Override
1149   public void newLink_actionPerformed(ActionEvent e)
1150   {
1151     GSequenceLink link = new GSequenceLink();
1152     boolean valid = false;
1153     while (!valid)
1154     {
1155       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1156               MessageManager.getString("label.new_sequence_url_link"),
1157               JvOptionPane.OK_CANCEL_OPTION, -1,
1158               null) == JvOptionPane.OK_OPTION)
1159       {
1160         if (link.checkValid())
1161         {
1162           if (((UrlLinkTableModel) linkUrlTable.getModel())
1163                   .isUniqueName(link.getName()))
1164           {
1165             ((UrlLinkTableModel) linkUrlTable.getModel())
1166                     .insertRow(link.getName(), link.getURL());
1167             valid = true;
1168           }
1169           else
1170           {
1171             link.notifyDuplicate();
1172             continue;
1173           }
1174         }
1175       }
1176       else
1177       {
1178         break;
1179       }
1180     }
1181   }
1182
1183   @Override
1184   public void editLink_actionPerformed(ActionEvent e)
1185   {
1186     GSequenceLink link = new GSequenceLink();
1187
1188     int index = linkUrlTable.getSelectedRow();
1189     if (index == -1)
1190     {
1191       // button no longer enabled if row is not selected
1192       Cache.debug("Edit with no row selected in linkUrlTable");
1193       return;
1194     }
1195
1196     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1197             .getNameColumn();
1198     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
1199             .getUrlColumn();
1200     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
1201     link.setName(oldName);
1202     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
1203
1204     boolean valid = false;
1205     while (!valid)
1206     {
1207       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
1208               MessageManager.getString("label.edit_sequence_url_link"),
1209               JvOptionPane.OK_CANCEL_OPTION, -1,
1210               null) == JvOptionPane.OK_OPTION)
1211       {
1212         if (link.checkValid())
1213         {
1214           if ((oldName.equals(link.getName()))
1215                   || (((UrlLinkTableModel) linkUrlTable.getModel())
1216                           .isUniqueName(link.getName())))
1217           {
1218             linkUrlTable.setValueAt(link.getName(), index, nameCol);
1219             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
1220             valid = true;
1221           }
1222           else
1223           {
1224             link.notifyDuplicate();
1225             continue;
1226           }
1227         }
1228       }
1229       else
1230       {
1231         break;
1232       }
1233     }
1234   }
1235
1236   @Override
1237   public void deleteLink_actionPerformed(ActionEvent e)
1238   {
1239     int index = linkUrlTable.getSelectedRow();
1240     int modelIndex = -1;
1241     if (index == -1)
1242     {
1243       // button no longer enabled if row is not selected
1244       Cache.debug("Delete with no row selected in linkUrlTable");
1245       return;
1246     }
1247     else
1248     {
1249       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1250     }
1251
1252     // make sure we use the model index to delete, and not the table index
1253     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1254   }
1255
1256   @Override
1257   public void defaultBrowser_mouseClicked(MouseEvent e)
1258   {
1259     // TODO: JAL-3048 not needed for j2s
1260     if (!Platform.isJS()) // BH 2019
1261     /**
1262      * Java only
1263      *
1264      * @j2sIgnore
1265      */
1266     {
1267       JFileChooser chooser = new JFileChooser(".");
1268       chooser.setDialogTitle(
1269               MessageManager.getString("label.select_default_browser"));
1270
1271       int value = chooser.showOpenDialog(this);
1272
1273       if (value == JFileChooser.APPROVE_OPTION)
1274       {
1275         defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1276       }
1277     }
1278   }
1279
1280   /*
1281    * (non-Javadoc)
1282    *
1283    * @see
1284    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1285    * .ActionEvent)
1286    */
1287   @Override
1288   protected void showunconserved_actionPerformed(ActionEvent e)
1289   {
1290     // TODO Auto-generated method stub
1291     super.showunconserved_actionPerformed(e);
1292   }
1293
1294   public static List<String> getGroupURLLinks()
1295   {
1296     return groupURLLinks;
1297   }
1298
1299   @Override
1300   public void minColour_actionPerformed(JPanel panel)
1301   {
1302     JalviewColourChooser.showColourChooser(this,
1303             MessageManager.getString("label.select_colour_minimum_value"),
1304             panel);
1305   }
1306
1307   @Override
1308   public void maxColour_actionPerformed(JPanel panel)
1309   {
1310     JalviewColourChooser.showColourChooser(this,
1311             MessageManager.getString("label.select_colour_maximum_value"),
1312             panel);
1313   }
1314
1315   @Override
1316   public void gapColour_actionPerformed(JPanel gap)
1317   {
1318     if (!useLegacyGap.isSelected())
1319     {
1320       JalviewColourChooser.showColourChooser(this,
1321               MessageManager.getString("label.select_gap_colour"), gap);
1322     }
1323   }
1324
1325   @Override
1326   public void hiddenColour_actionPerformed(JPanel hidden)
1327   {
1328     JalviewColourChooser.showColourChooser(this,
1329             MessageManager.getString("label.select_hidden_colour"), hidden);
1330   }
1331
1332   @Override
1333   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1334   {
1335     boolean enabled = useLegacyGap.isSelected();
1336     if (enabled)
1337     {
1338       gapColour.setBackground(
1339               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1340     }
1341     else
1342     {
1343       gapColour.setBackground(
1344               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1345     }
1346     gapColour.setEnabled(!enabled);
1347     gapLabel.setEnabled(!enabled);
1348   }
1349
1350   @Override
1351   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1352   {
1353     useLegacyGap.setSelected(false);
1354     useLegacyGaps_actionPerformed(null);
1355     showHiddenAtStart.setSelected(false);
1356     hiddenColour.setBackground(
1357             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1358   }
1359
1360   @Override
1361   protected void userIdWidth_actionPerformed()
1362   {
1363     try
1364     {
1365       String val = userIdWidth.getText().trim();
1366       if (val.length() > 0)
1367       {
1368         Integer iw = Integer.parseInt(val);
1369         if (iw.intValue() < 12)
1370         {
1371           throw new NumberFormatException();
1372         }
1373         userIdWidth.setText(iw.toString());
1374       }
1375     } catch (NumberFormatException x)
1376     {
1377       userIdWidth.setText("");
1378       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1379               MessageManager
1380                       .getString("warn.user_defined_width_requirements"),
1381               MessageManager.getString("label.invalid_id_column_width"),
1382               JvOptionPane.WARNING_MESSAGE);
1383     }
1384   }
1385
1386   @Override
1387   protected void autoIdWidth_actionPerformed()
1388   {
1389     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1390     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1391   }
1392
1393   /**
1394    * Returns true if structure viewer path is to a valid executable, else shows an
1395    * error dialog. Does nothing if the path is empty, as is the case for Jmol
1396    * (built in to Jalview) or when Jalview is left to try default paths.
1397    */
1398   private boolean validateViewerPath()
1399   {
1400     if (structureViewerPath.getText().trim().length() > 0)
1401     {
1402       File f = new File(structureViewerPath.getText());
1403       if (!f.canExecute())
1404       {
1405         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1406                 MessageManager.getString("label.invalid_viewer_path"),
1407                 MessageManager.getString("label.invalid_viewer_path"),
1408                 JvOptionPane.ERROR_MESSAGE);
1409         return false;
1410       }
1411     }
1412     return true;
1413   }
1414
1415   /**
1416    * If Chimera or ChimeraX or Pymol is selected, check it can be found on default
1417    * or user-specified path, if not show a warning/help dialog
1418    */
1419   @Override
1420   protected void structureViewer_actionPerformed(String selectedItem)
1421   {
1422     if (selectedItem.equals(ViewerType.JMOL.name()))
1423     {
1424       structureViewerPath.setEnabled(false);
1425       structureViewerPathLabel.setEnabled(false);
1426       return;
1427     }
1428     boolean found = false;
1429     structureViewerPath.setEnabled(true);
1430     structureViewerPathLabel.setEnabled(true);
1431     structureViewerPathLabel.setText(MessageManager
1432             .formatMessage("label.viewer_path", selectedItem));
1433
1434     /*
1435      * Try user-specified and standard paths for structure viewer executable
1436      */
1437     String viewerPath = "";
1438     List<String> paths = null;
1439     try
1440     {
1441       ViewerType viewerType = ViewerType.valueOf(selectedItem);
1442       switch (viewerType)
1443       {
1444       case JMOL:
1445         // dealt with above
1446         break;
1447       case CHIMERA:
1448         viewerPath = Cache.getDefault(CHIMERA_PATH, "");
1449         paths = StructureManager.getChimeraPaths(false);
1450         break;
1451       case CHIMERAX:
1452         viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
1453         paths = StructureManager.getChimeraPaths(true);
1454         break;
1455       case PYMOL:
1456         viewerPath = Cache.getDefault(PYMOL_PATH, "");
1457         paths = PymolManager.getPymolPaths();
1458         break;
1459       }
1460     } catch (IllegalArgumentException e)
1461     {
1462       // only valid entries should be in the drop-down
1463     }
1464     structureViewerPath.setText(viewerPath);
1465
1466     paths.add(0, structureViewerPath.getText());
1467     for (String path : paths)
1468     {
1469       if (new File(path.trim()).canExecute())
1470       {
1471         found = true;
1472         break;
1473       }
1474     }
1475
1476     if (!found)
1477     {
1478       String[] options = { "OK", "Help" };
1479       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1480               JvSwingUtils.wrapTooltip(true,
1481                       MessageManager.getString("label.viewer_missing")),
1482               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1483               null, options, options[0]);
1484
1485       if (showHelp == JvOptionPane.NO_OPTION)
1486       {
1487         this.selectTab(Preferences.TabRef.STRUCTURE_TAB, null);
1488         try
1489         {
1490           Help.showHelpWindow(HelpId.StructureViewer);
1491         } catch (HelpSetException e)
1492         {
1493           e.printStackTrace();
1494         }
1495       }
1496       else if (showHelp == JvOptionPane.OK_OPTION)
1497       {
1498         this.selectTab(Preferences.TabRef.STRUCTURE_TAB, null);
1499         CompletableFuture<Void> cf = CompletableFuture.runAsync(() -> {
1500           try
1501           {
1502             for (int i = 0; i < 3; i++)
1503             {
1504               structureViewerPath.setBackground(Color.PINK);
1505               Thread.sleep(500);
1506               structureViewerPath.setBackground(Color.WHITE);
1507               Thread.sleep(500);
1508             }
1509           } catch (InterruptedException e)
1510           {
1511           }
1512         });
1513       }
1514     }
1515   }
1516
1517   public class OptionsParam
1518   {
1519     private String name;
1520
1521     private String code;
1522
1523     public OptionsParam(String name, String code)
1524     {
1525       this.name = name;
1526       this.code = code;
1527     }
1528
1529     public String getName()
1530     {
1531       return name;
1532     }
1533
1534     public void setName(String name)
1535     {
1536       this.name = name;
1537     }
1538
1539     public String getCode()
1540     {
1541       return code;
1542     }
1543
1544     public void setCode(String code)
1545     {
1546       this.code = code;
1547     }
1548
1549     @Override
1550     public String toString()
1551     {
1552       return name;
1553     }
1554
1555     @Override
1556     public boolean equals(Object that)
1557     {
1558       if (!(that instanceof OptionsParam))
1559       {
1560         return false;
1561       }
1562       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1563     }
1564
1565     @Override
1566     public int hashCode()
1567     {
1568       return name.hashCode() + code.hashCode();
1569     }
1570   }
1571
1572   private class UrlListSelectionHandler implements ListSelectionListener
1573   {
1574
1575     @Override
1576     public void valueChanged(ListSelectionEvent e)
1577     {
1578       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1579
1580       int index = lsm.getMinSelectionIndex();
1581       if (index == -1)
1582       {
1583         // no selection, so disable delete/edit buttons
1584         editLink.setEnabled(false);
1585         deleteLink.setEnabled(false);
1586         return;
1587       }
1588       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1589
1590       // enable/disable edit and delete link buttons
1591       if (((UrlLinkTableModel) linkUrlTable.getModel())
1592               .isRowDeletable(modelIndex))
1593       {
1594         deleteLink.setEnabled(true);
1595       }
1596       else
1597       {
1598         deleteLink.setEnabled(false);
1599       }
1600
1601       if (((UrlLinkTableModel) linkUrlTable.getModel())
1602               .isRowEditable(modelIndex))
1603       {
1604         editLink.setEnabled(true);
1605       }
1606       else
1607       {
1608         editLink.setEnabled(false);
1609       }
1610     }
1611   }
1612 }